Status
[December 2020] The genome sequence of Fusarium oxysporum f.sp. cubense II5 were not determined by the Joint Genome Institute (JGI), but were provided by Li-Jun Ma and Yong Zhang on Oct 14, 2020. This genome was sequenced with PacBio and illumina, assembled with Canu v1.8 followed by polishing by Quiver using Illumina sequences, and annotated with the JGI Annotation Pipeline.
Summary statistics for the Fusarium oxysporum f.sp.
cubense II5 v2.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 49.43 |
| Sequencing read coverage depth | 341.0x |
| # of contigs | 67 |
| # of scaffolds | 53 |
| # of scaffolds >= 2Kbp | 53 |
| Scaffold N50 | 5 |
| Scaffold L50 (Mbp) | 4.48 |
| # of gaps | 14 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 6.69, 6.51, 5.26 |
RNA was obtained from an infection time course experiment. The presence of host cell RNA accounts for the poor mapping statistics below.
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 1104761 | 33247 | 3.0% |
| Ests | est.fasta | 141461436 | 51469578 | 36.4% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1775 | 1567 |
| transcript | 1626 | 1431 |
| exon | 555 | 344 |
| intron | 80 | 56 |
| description: | ||
| protein length (aa) | 469 | 400 |
| exons per gene | 2.93 | 2 |
| # of gene models | 16048 |
Collaborators
- Li-Jun Ma, University of Massachusetts Amherst, USA
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Zhang Y, Liu S, Mostert D, Yu H, Zhuo M, Li G, Zuo C, Haridas S, Webster K, Li M, Grigoriev IV, Yi G, Viljoen A, Li C, Ma LJ
Virulence of banana wilt-causing fungal pathogen Fusarium oxysporum tropical race 4 is mediated by nitric oxide biosynthesis and accessory genes.
Nat Microbiol. 2024 Aug 16;():. doi: 10.1038/s41564-024-01779-7
Zhang Y, Liu S, Mostert D, Yu H, Zhuo M, Li G, Zuo C, Haridas S, Webster K, Li M, Grigoriev IV, Yi G, Viljoen A, Li C, Ma LJ
Virulence of banana wilt-causing fungal pathogen Fusarium oxysporum tropical race 4 is mediated by nitric oxide biosynthesis and accessory genes.
Nat Microbiol. 2024 Aug 16;():. doi: 10.1038/s41564-024-01779-7
Links
- JGI EcoGroup Portals: Plant Pathogens
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Sordariomycetes Hypocreomycetidae Hypocreales Nectriaceae Fusarium
Funding
The work conducted by the U.S. Department of Energy Joint Genome
Institute, a DOE Office of Science User Facility, is supported by
the Office of Science of the U.S. Department of Energy under
Contract No. DE-AC02-05CH11231.
